Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_092345435.1 BLU87_RS05345 1-pyrroline-5-carboxylate dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >NCBI__GCF_900107645.1:WP_092345435.1 Length = 373 Score = 357 bits (915), Expect = e-103 Identities = 178/365 (48%), Positives = 248/365 (67%), Gaps = 2/365 (0%) Query: 28 ATYKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSN 87 A +P NEP YA GSP+R+ L+ AL ++ + VPL+I GKEV++ +++ + Sbjct: 7 AAINIPSPQNEPVLAYAPGSPERQKLKLALEEL-KSKQIEVPLIIGGKEVRTGNTVKIAC 65 Query: 88 PASHG-PVATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDV 146 P H + T A K+VQ AI++A+ A+ +W S + +RA++FLKAADL++ YR+ + Sbjct: 66 PHDHSIQLGTSHKAGPKEVQMAIDAAMAAKPAWQSLRWEERAAIFLKAADLLAGPYRFLI 125 Query: 147 MALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEG 206 A TM KN +QAEID+A EL DF RF V +A+++YA QP+H +WN V++RPLEG Sbjct: 126 NAATMLNISKNPFQAEIDAACELIDFLRFNVYFAQEVYADQPLHSPSPIWNYVQHRPLEG 185 Query: 207 FVYAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFV 266 FV+A++PFNFTAI GNL APA+MGN VVWKP+ SA+ + + ++L EAGLP VI FV Sbjct: 186 FVFAVAPFNFTAIAGNLPTAPAIMGNTVVWKPASSAVYAPYHFMKLLQEAGLPDGVINFV 245 Query: 267 PGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNF 326 PG +V LD PDF +HFTGST VF++++ QI +AA KY++YPRIVGETGGK+F Sbjct: 246 PGSGSDVGNVCLDSPDFNGIHFTGSTAVFQSMWKQIGNNIAANKYKTYPRIVGETGGKDF 305 Query: 327 HLIHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPP 386 H SAD++ A VRGAFEYQGQKCSA SR YV S+ + L ++ ++ +K+G Sbjct: 306 IFAHSSADVKALATGIVRGAFEYQGQKCSAASRAYVPESLWEPVLTEIKAQTDRIKMGDV 365 Query: 387 SDFTN 391 +DF N Sbjct: 366 ADFRN 370 Lambda K H 0.316 0.130 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 620 Number of extensions: 30 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 572 Length of database: 373 Length adjustment: 33 Effective length of query: 539 Effective length of database: 340 Effective search space: 183260 Effective search space used: 183260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory